The crease is an occupational hazard I'm afraid...
Doesn't happen on all the boxes, depends on where exactly I had to position the lid strut for it to function properly. A few millimeters either way does make a difference.
All the boxes are hand made and very slightly different.

One solution would be to cut a small rectangular piece out of the top layer of latherette/foam in that corner to make a little 'garage' for the folded arm.

Well, Karl was nice enough to send me a piece of leatherette, so I could cut the top left corner of the box's inside (2/3 height) and place a little piece of leatherette on the "new bottom" (for cosmetic purpose).
Now, the articulated arm gets gently into its new customized hole.